Contacts of the helix formed by residues 16 - 34 (chain D) in PDB entry 3IML
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 16 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.5 21.0 - - + +
13D SER* 3.1 19.6 + - - +
15D GLY* 1.3 75.9 - - - +
17D PRO* 1.3 76.2 - - + +
18D ASP* 3.1 50.2 + - - +
19D LYS* 2.9 7.1 + - - -
20D VAL* 2.8 25.5 + - - +
167D ASP* 3.3 15.5 + - - +
169D LYS* 3.8 41.0 + - + +
249D LYS* 3.6 13.6 - - - -
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Residues in contact with PRO 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY 3.9 2.5 - - - +
16D HIS* 1.3 99.3 - - + +
18D ASP* 1.3 61.2 + - - +
20D VAL* 3.4 12.0 + - + +
21D ALA* 3.2 18.5 + - - +
47D CYS* 3.7 2.1 - - - -
167D ASP* 3.7 16.4 - - - +
238D GLY* 3.8 10.1 - - - +
239D PRO* 3.9 12.8 - - + -
242D ASP* 3.5 38.1 - - + +
243D CYS 4.5 2.0 - - - +
244D GLY* 3.5 21.8 - - - +
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Residues in contact with ASP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 5.6 0.9 - - - +
16D HIS* 3.1 18.7 + - + +
17D PRO* 1.3 78.8 - - - +
19D LYS* 1.3 57.1 + - - +
21D ALA* 3.4 5.9 - - - +
22D ASP* 3.1 28.8 + - - +
243D CYS 3.9 5.4 - - - +
244D GLY* 3.2 6.9 - - - -
245D LEU* 3.0 33.4 + - - +
248D ARG* 4.0 20.2 + - + +
249D LYS* 2.7 40.5 + - + -
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 3.7 20.9 - - + +
13D SER 3.5 22.0 - - - +
14D GLU 4.2 0.2 - - - +
16D HIS* 2.9 10.1 + - - +
18D ASP* 1.3 75.7 - - - +
20D VAL* 1.3 60.5 + - - +
21D ALA 3.2 1.3 - - - -
22D ASP* 3.0 26.8 + - - +
23D GLN* 2.8 41.1 + - - +
249D LYS* 4.0 17.3 - - + -
252D VAL* 4.3 11.7 - - - -
253D ASP* 2.8 29.4 + - - -
359D ALA* 2.6 34.7 + - - +
360D ALA* 4.1 15.0 - - + +
361D TYR 5.0 2.5 - - - +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU 3.7 12.6 - - - +
15D GLY* 3.7 15.0 - - - +
16D HIS 2.8 20.5 + - - +
17D PRO* 3.6 10.5 - - + +
19D LYS* 1.3 74.7 - - - +
21D ALA* 1.3 57.7 + - - +
23D GLN* 3.2 9.7 + - - +
24D ILE* 2.9 50.3 + - + +
47D CYS* 4.2 11.2 - - - -
74D ILE* 4.2 13.7 - - + -
77D ILE* 4.1 15.8 - - + +
79D TYR* 4.2 12.6 - - + -
239D PRO* 4.3 9.9 - - + -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO 3.2 9.2 + - - +
18D ASP 3.4 10.5 - - - +
20D VAL* 1.3 76.6 - - - +
22D ASP* 1.3 65.3 + - - +
24D ILE 3.3 0.3 + - - -
25D SER* 2.9 27.0 + - - -
45D THR* 3.6 23.5 - - - +
47D CYS* 4.1 6.7 - - - -
244D GLY 4.1 4.0 - - - +
245D LEU* 3.5 27.8 - - - +
246D THR* 3.4 6.0 + - - +
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Residues in contact with ASP 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ASP 3.1 19.6 + - - +
19D LYS* 3.0 38.5 + - - +
21D ALA* 1.3 74.3 - - - +
23D GLN* 1.3 58.0 + - - +
25D SER* 3.3 5.0 - - - -
26D ASP* 2.9 26.0 + - - +
246D THR* 3.6 1.2 + - - +
247D GLY* 2.9 30.1 + - - -
248D ARG 4.9 0.2 + - - -
249D LYS* 4.3 8.1 + - - +
253D ASP* 4.3 7.1 - - - +
267D SER* 3.4 34.4 + - - +
359D ALA* 3.9 5.2 - - - +
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 2.8 47.5 + - - +
19D LYS* 2.8 28.7 + - - +
20D VAL 3.6 3.1 - - - +
22D ASP* 1.3 73.8 - - - +
24D ILE* 1.3 60.8 + - - +
26D ASP 3.7 0.6 - - - +
27D ALA* 2.8 31.2 + - - +
73D THR* 4.0 14.6 - - + -
76D ARG* 2.8 27.1 + - - +
77D ILE* 3.6 6.3 - - + +
356D GLU* 3.9 10.0 - - + +
359D ALA* 3.4 26.0 - - + +
360D ALA* 3.8 12.1 - - - +
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Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 2.9 30.5 + - + +
21D ALA* 3.3 4.2 + - - +
23D GLN* 1.3 71.5 - - - +
25D SER* 1.3 68.6 + - - +
27D ALA* 3.2 3.4 + - - +
28D ILE* 3.0 30.2 + - + +
45D THR* 3.7 28.9 - - + +
47D CYS* 5.0 2.7 - - + -
52D VAL* 4.2 11.4 - - + -
54D LEU* 3.9 15.0 - - + -
70D ALA* 4.1 18.4 - - + +
73D THR* 4.1 23.6 - - + -
74D ILE* 4.0 28.9 - - + -
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA 2.9 12.6 + - - -
22D ASP 3.3 6.1 - - - -
24D ILE* 1.3 78.0 - - - +
26D ASP* 1.3 57.9 + - - -
28D ILE* 3.4 5.7 + - - +
29D LEU* 3.1 22.9 + - - +
43D ALA* 2.6 34.5 + - - +
45D THR* 3.0 11.2 + - - -
246D THR* 2.7 26.6 + - - +
268D GLY* 3.8 16.7 - - - -
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Residues in contact with ASP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP 2.9 14.5 + - - +
23D GLN 4.2 0.9 - - - +
24D ILE 3.3 0.2 - - - -
25D SER* 1.3 70.6 - - - +
27D ALA* 1.3 59.4 + - - +
28D ILE 3.2 1.6 - - - -
29D LEU* 3.3 9.7 + - - +
30D ASP* 2.9 32.1 + - - -
267D SER* 2.9 27.7 + - - -
268D GLY 2.8 19.9 + - - -
276D ARG* 2.9 33.7 + - - -
355D TYR* 3.5 22.7 - - - +
356D GLU* 3.6 10.5 - - - +
358D THR* 3.8 0.2 + - - -
359D ALA* 3.8 5.4 - - + +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN 2.8 22.8 + - - +
24D ILE 3.6 4.5 - - - +
26D ASP* 1.3 73.4 - - - +
28D ILE* 1.3 57.4 + - - +
30D ASP* 4.0 3.5 - - - +
31D ALA* 3.1 27.4 + - - +
69D ILE* 3.6 13.8 - - + +
73D THR* 3.2 24.5 - - - +
356D GLU* 3.4 24.7 - - - +
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 3.0 29.0 + - + +
25D SER* 3.6 7.4 - - - +
27D ALA* 1.3 76.1 - - - +
29D LEU* 1.3 63.4 + - - +
31D ALA* 3.5 3.3 + - - +
32D ILE* 3.0 47.4 + - + +
43D ALA* 4.5 7.6 - - + -
54D LEU* 3.9 20.2 - - + -
58D ILE* 4.8 0.4 - - + -
64D ILE* 5.7 0.4 - - + -
66D TYR* 4.0 26.2 - - + +
69D ILE* 3.9 20.6 - - + -
70D ALA* 5.2 0.2 - - + -
97D TYR* 3.0 36.3 - - + +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D SER 3.1 13.6 + - - +
26D ASP* 3.3 14.8 + - - +
28D ILE* 1.3 74.2 - - - +
30D ASP* 1.3 66.8 + - - +
32D ILE* 3.1 7.8 + - - +
33D LEU* 2.8 45.2 + - + +
41D VAL* 3.6 39.7 - - + +
268D GLY* 4.9 1.1 - - - -
269D LYS 3.1 26.5 - - - +
270D ASP* 3.9 12.6 - - + +
276D ARG* 3.5 17.5 - - - +
355D TYR* 3.8 19.7 - - + -
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Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP 2.9 16.5 + - - +
27D ALA* 4.0 4.9 - - - +
28D ILE 3.4 0.2 - - - -
29D LEU* 1.3 73.8 - - - +
31D ALA* 1.3 54.8 - - - +
33D LEU* 3.0 1.5 + - - +
34D ALA* 2.7 36.8 + - - +
353D PRO* 3.1 39.3 - - + +
354D ILE 3.2 1.0 + - - -
355D TYR* 2.8 30.1 + - - +
356D GLU* 2.9 32.7 + - - +
357D LYS 4.8 0.2 + - - -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA 3.1 13.9 + - - +
28D ILE 3.8 4.0 - - - +
29D LEU 3.3 0.2 - - - -
30D ASP* 1.3 77.8 - - - +
32D ILE* 1.3 60.2 + - - +
34D ALA* 3.9 11.4 + - - +
35D GLN* 3.9 9.4 + - - +
64D ILE* 3.2 22.0 - - + +
69D ILE* 3.2 36.1 - - + -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 3.0 37.0 + - + +
29D LEU 3.5 4.0 - - - +
31D ALA* 1.3 75.7 - - - +
33D LEU* 1.3 61.7 + - + +
35D GLN* 3.2 5.7 + - - +
36D ASP* 2.8 23.7 + - - +
39D SER* 3.3 33.4 - - - +
41D VAL* 3.9 23.3 - - + -
58D ILE* 4.1 22.2 - - + -
60D THR* 3.4 12.8 - - + +
62D ALA* 3.9 7.9 - - + +
64D ILE* 3.9 17.7 - - + -
66D TYR* 4.5 5.2 - - + +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 2.8 52.7 + - + +
30D ASP 3.8 2.5 - - - +
32D ILE* 1.3 70.9 - - + +
34D ALA* 1.3 64.5 + - - +
35D GLN 3.2 0.7 + - - -
36D ASP 3.5 15.4 + - - +
37D LYS* 3.6 39.9 + - + +
39D SER* 4.5 16.8 - - - +
271D PRO* 4.5 12.8 - - + -
351D LEU* 5.2 0.7 - - + -
352D ARG 3.6 27.4 - - - +
353D PRO* 4.4 15.1 - - + +
355D TYR* 3.9 13.9 - - + -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ASP 2.7 21.4 + - - +
31D ALA* 4.0 8.3 - - - +
32D ILE 3.2 0.2 - - - -
33D LEU* 1.3 74.5 - - - +
35D GLN* 1.3 59.5 + - + +
353D PRO* 4.3 19.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il